Mon Oct 10 14:40:20 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:40:20 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6704963 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -21.78100 31.31400 ymin,ymax (A): 12.10400 57.99800 zmin,zma (A): 27.96100 78.26200 x,y,z range (A): 53.09500 45.89400 50.30100 scale (grids/A): 0.6704963 object centre (A): 4.766500 35.05100 53.11150 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.5852 centred at (gu) : 89.38494 90.68555 90.31398 assigned negative charge : -362.0858 centred at (gu) : 89.56516 90.67487 90.39323 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7213 nv = 96 ne = 84 npr = 49061 no. pairs analyzed = 49061 no. exposed pairs = 2906 no. arc points = 20542 no. surface atoms = 990 nbur = 1374 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 436 mr = 4040 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2900000 number of dielectric boundary points 3537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1912 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8396 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4582264E-09 -3.3257919E-08 midg,1,midg; midg,igrid,midg -1.2679707E-08 -1.0743690E-08 1,midg,midg; igrid,midg,midg 3.4879658E-08 -4.9437727E-08 gauss-seidel spectral radius is 0.9884497 estimated iterations to convergence 76 setup time was (sec) 0.5700000 now iterating at: 14:40:20 rms-change max change #iterations 0.1713768 24.60653 at 10iterations 1.9252321E-02 2.937607 at 20iterations 2.1474634E-03 0.2846663 at 30iterations 2.6000172E-04 4.3320656E-02 at 40iterations 4.1551812E-05 8.4495544E-03 at 50iterations finished qdiffx linear iterations at : 14:40:23 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 4.1551812E-05 8.4495544E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:40:24 3.354u 0.192s 0:04.04 87.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:40:24 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.011489 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -21.78100 31.31400 ymin,ymax (A): 12.10400 57.99800 zmin,zma (A): 27.96100 78.26200 x,y,z range (A): 53.09500 45.89400 50.30100 scale (grids/A): 2.011489 object centre (A): 4.766500 35.05100 53.11150 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.5852 centred at (gu) : 88.15438 92.05635 90.94151 assigned negative charge : -362.0858 centred at (gu) : 88.69533 92.02451 91.17952 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77017 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20542 grid for indexing accessible points = 1.400000 m= 28978 mr = 53730 m= 5321 mr = 21592 m= 435 mr = 3520 m= 8 mr = 203 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 551 time to turn everything in is 0.5600000 number of dielectric boundary points 32714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17655 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6704963 object centre at (A) : 4.766500 35.05100 53.11150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8515509E-02 -4.3153994E-02 midg,1,midg; midg,igrid,midg -1.1565170E-02 -4.8748252E-04 1,midg,midg; igrid,midg,midg 3.1668469E-02 -6.1531165E-03 gauss-seidel spectral radius is 0.9987499 estimated iterations to convergence 224 setup time was (sec) 0.8600000 now iterating at: 14:40:25 rms-change max change #iterations 4.541607 201.1902 at 10iterations 2.194841 70.91325 at 20iterations 1.055974 33.03629 at 30iterations 0.5119494 15.53412 at 40iterations 0.2475618 7.356607 at 50iterations 0.1196956 3.421051 at 60iterations 5.7791010E-02 1.813644 at 70iterations 2.8062893E-02 0.8786602 at 80iterations 1.3568592E-02 0.3968275 at 90iterations 6.5687294E-03 0.1839739 at 100iterations 3.2084028E-03 9.0898514E-02 at 110iterations 1.5537398E-03 4.5287609E-02 at 120iterations finished qdiffx linear iterations at : 14:40:31 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 1.5537398E-03 4.5287609E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 14:40:32 7.507u 0.210s 0:08.04 95.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:40:32 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.017233 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -21.78100 31.31400 ymin,ymax (A): 12.10400 57.99800 zmin,zma (A): 27.96100 78.26200 x,y,z range (A): 53.09500 45.89400 50.30100 scale (grids/A): 3.017233 object centre (A): 4.766500 35.05100 53.11150 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.5852 centred at (gu) : 87.23144 93.08427 91.41224 assigned negative charge : -362.0858 centred at (gu) : 88.04298 93.03686 91.76926 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 177975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20542 grid for indexing accessible points = 1.400000 m= 91519 mr = 129844 m= 35789 mr = 75448 m= 10047 mr = 29127 m= 1880 mr = 7786 m= 174 mr = 1346 m= 5 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 1885 time to turn everything in is 1.460000 number of dielectric boundary points 73755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 17848 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.011489 object centre at (A) : 4.766500 35.05100 53.11150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4235779 -0.2390237 midg,1,midg; midg,igrid,midg -3.7365399E-02 0.1312598 1,midg,midg; igrid,midg,midg 0.3313484 1.4000671E-02 gauss-seidel spectral radius is 0.9992816 estimated iterations to convergence 294 setup time was (sec) 1.760000 now iterating at: 14:40:34 rms-change max change #iterations 10.45569 336.3209 at 10iterations 6.155000 148.1627 at 20iterations 3.614786 71.36126 at 30iterations 2.115568 46.88096 at 40iterations 1.234016 27.12769 at 50iterations 0.7205931 12.67277 at 60iterations 0.4203483 8.290378 at 70iterations 0.2443705 4.738739 at 80iterations 0.1417729 2.763272 at 90iterations 8.2538798E-02 1.505308 at 100iterations 4.7915358E-02 0.7845993 at 110iterations 2.7921349E-02 0.5553231 at 120iterations 1.6200671E-02 0.2925987 at 130iterations 9.4221560E-03 0.1545458 at 140iterations 5.5019232E-03 9.5844269E-02 at 150iterations 3.2270278E-03 5.6819916E-02 at 160iterations 1.9030037E-03 3.4752369E-02 at 170iterations 1.1402837E-03 2.2537231E-02 at 180iterations finished qdiffx linear iterations at : 14:40:45 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 1.1402837E-03 2.2537231E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 14:40:45 12.912u 0.204s 0:13.40 97.8% 0+0k 0+0io 0pf+0w